Purpose:

To determine the DGE profiles (for mouse genes), relative to uninfected controls, of self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV or co-infected with HBV/HDV at 8 and 28 days post-infection. This run includes the samples sequenced in July 2018.

library(dplyr)
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library(stringr)
library(ggplot2)
library(reshape2)
library(openxlsx)
library(DESeq2)
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library(dplyr)
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library(stringr)
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library(data.table)
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library(genefilter)
library(ggrepel)
library(viridis)
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source("http://bioconductor.org/biocLite.R")
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biocLite("org.Mm.eg.db")
## BioC_mirror: https://bioconductor.org
## Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
## Installing package(s) 'org.Mm.eg.db'
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require(org.Mm.eg.db)
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## Loading required package: AnnotationDbi
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##     select
## 

Function to perform DGE analysis with both donor and treatment set as factors influencing the counts.

DGE_analysis <- function(sampledirectory) {
a <- basename(Sys.glob(file.path(sampledirectory, "*.txt")))
sample_names <- sub('.txt', '', a)
##Here the donors are renamed based off the Hurel names (i.e. HU___) - RNASeq reads were all 
##named using a different ID system.
sampleTable <- data.frame(sampleName = sample_names, sampleFile = a, treatment = 
    ifelse(grepl("Ctrl", a), "mock", ifelse(grepl("*co|*HDV", a),"coinf", "HBV")), 
   donor = ifelse(grepl("BD330*", a), "HU1019", 
                  ifelse(grepl("BD405*", a), "HU1020", 
                            ifelse(grepl("HU1016*", a), "HU1016", "HU1007"))),
   time = ifelse(grepl("*D8|Day 8", a), "d8", "d28"), 
   replicate = ifelse(grepl("*sample_1h|*D8_ah|*D8_aa|*D8_am|*sample_1m", a), "a",
          ifelse(grepl("*sample_2h|D28_bh|D28_ba|D28_bm|*sample_2m", a), "b", 
           ifelse(grepl("*sample_3h| * sample 1h|* sample 1m", a), "c",
            ifelse(grepl("* sample 2h|* sample 2m", a), "d",
             ifelse(grepl("* sample 3h|* sample 3m", a), "e", ""))))))
dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = sampledirectory, 
                                  design = ~donor + treatment)
dds
dds@colData
contrast <- c("treatment", levels(sampleTable$treatment))
output_basename <- sprintf("%s-%s_vs_%s_%s_analysis", "Mousegenes", contrast[2], 
                           contrast[3], levels(sampleTable$time))
output_basename
dds <- estimateSizeFactors(dds)
dds@colData
dds <- estimateDispersions(dds)

plotDispEsts(dds, main=sprintf("%s Dispersion Estimates", output_basename))
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast=contrast)
res <- res[order(res$padj, -abs(res$log2FoldChange)),]
mcols(res, use.names=TRUE)
##Log-intensity ratios = M values, log-intensity averages = A values
##Red points indicate padj < 0.1. 
plotMA(res, alpha=0.1, main=sprintf(output_basename))
attr(res, "filterThreshold")

metadata(res)$alpha
metadata(res)$filterThreshold
plot(metadata(res)$filterNumRej,
     type="b", ylab="number of rejections",
     xlab="quantiles of filter")
lines(metadata(res)$lo.fit, col="red")
abline(v=metadata(res)$filterTheta)

key = "ENSEMBL"
cols = c("ENTREZID", "SYMBOL", "GENENAME", "ALIAS", "REFSEQ", "ACCNUM")
for (col in cols) {
  # Get annotation data for column
  annotation_data <- AnnotationDbi::select(org.Mm.eg.db, rownames(res), col, keytype=key)
  # Collapse one-to-many relationships
  tmp <- aggregate(annotation_data[col], by=annotation_data[key],
                   # to a list
                   FUN=function(x)list(x))
  # Match on key and append to results
  idx <- match(rownames(res), tmp[[key]])
  res[[col]] <- tmp[idx,col]
}

output_data <- as.data.frame(res)
LIST_COLS <- sapply(output_data, is.list)
for (COL in colnames(output_data)[LIST_COLS]) {
  output_data[COL] <-
    sapply(output_data[COL],
           function(x)sapply(x, function(y) paste(unlist(y),
                                                  collapse=", ") ) )
}

# Save data frame above as tab-separated file
write.table(output_data,
            file=file.path("Mouse DGEs_donortreatment", paste(Sys.Date(), 
            "mouse_donor_treatment",output_basename, "_results.txt", sep='')), 
            quote=FALSE, sep="\t", row.names=TRUE, col.names=NA)
return(list(dds@colData, head(res)))
}


##For each timepoint, determine the DGE profile when comparing the different treatments 
##groups to one another (i.e. HBV-infected versus control).

##uninfected control cells versus those mono-infected with HBV
DGE_analysis("Mouse d8_ctrlvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 12 rows and 5 columns
##                            treatment    donor     time replicate
##                             <factor> <factor> <factor>  <factor>
## BD330_Ctrl_D8mousegenes         mock   HU1019       d8          
## BD330_HBV_D8mousegenes           HBV   HU1019       d8          
## BD405A_Ctrl_D8mousegenes        mock   HU1020       d8          
## BD405A_HBV_D8mousegenes          HBV   HU1020       d8          
## Ctrl_D8_sample_1mousegenes      mock   HU1007       d8         a
## ...                              ...      ...      ...       ...
## HBV_D8_sample_1mousegenes        HBV   HU1007       d8         a
## HBV_D8_sample_2mousegenes        HBV   HU1007       d8         b
## HBV_D8_sample_3mousegenes        HBV   HU1007       d8          
## HU1016 Ctrl D8mousegenes        mock   HU1016       d8          
## HU1016_B_D8mousegenes            HBV   HU1016       d8          
##                            sizeFactor
##                             <numeric>
## BD330_Ctrl_D8mousegenes     1.0522833
## BD330_HBV_D8mousegenes      0.7382776
## BD405A_Ctrl_D8mousegenes    0.7851726
## BD405A_HBV_D8mousegenes     0.7187235
## Ctrl_D8_sample_1mousegenes  1.1914770
## ...                               ...
## HBV_D8_sample_1mousegenes   1.4504736
## HBV_D8_sample_2mousegenes   0.9846915
## HBV_D8_sample_3mousegenes   1.4119102
## HU1016 Ctrl D8mousegenes    0.8937149
## HU1016_B_D8mousegenes       0.8234693
## 
## [[2]]
## log2 fold change (MAP): treatment HBV vs mock 
## Wald test p-value: treatment HBV vs mock 
## DataFrame with 6 rows and 12 columns
##                     baseMean log2FoldChange     lfcSE      stat
##                    <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000035385 1320.3139     -0.9589377 0.1549593 -6.188318
## ENSMUSG00000039518 6501.1613      0.8093483 0.1512841  5.349858
## ENSMUSG00000036144  243.2058     -1.0747784 0.2074015 -5.182114
## ENSMUSG00000027792  923.9060     -1.0579783 0.2040122 -5.185858
## ENSMUSG00000022231 1628.0571     -0.8301908 0.1675028 -4.956281
## ENSMUSG00000031072  202.3899      0.6575575 0.1438225  4.572006
##                          pvalue         padj ENTREZID SYMBOL
##                       <numeric>    <numeric>   <list> <list>
## ENSMUSG00000035385 6.080937e-10 6.764435e-06    20296   Ccl2
## ENSMUSG00000039518 8.802331e-08 4.895856e-04   386463   Cdsn
## ENSMUSG00000036144 2.193852e-07 6.101101e-04    17286  Meox2
## ENSMUSG00000027792 2.150227e-07 6.101101e-04    12038   Bche
## ENSMUSG00000022231 7.185525e-07 1.598636e-03    20356 Sema5a
## ENSMUSG00000031072 4.830778e-06 8.956263e-03    72284 Oraov1
##                                                                                                                                                       GENENAME
##                                                                                                                                                         <list>
## ENSMUSG00000035385                                                                                                              chemokine (C-C motif) ligand 2
## ENSMUSG00000039518                                                                                                                              corneodesmosin
## ENSMUSG00000036144                                                                                                                       mesenchyme homeobox 2
## ENSMUSG00000027792                                                                                                                       butyrylcholinesterase
## ENSMUSG00000022231 sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A
## ENSMUSG00000031072                                                                                                                 oral cancer overexpressed 1
##                                                    ALIAS
##                                                   <list>
## ENSMUSG00000035385                  AI323594,HC11,JE,...
## ENSMUSG00000039518                         AI747712,Cdsn
## ENSMUSG00000036144                AI528662,Gax,Mox-2,...
## ENSMUSG00000027792                    C730038G20Rik,Bche
## ENSMUSG00000022231 5930434A13,9130201M22Rik,AI464145,...
## ENSMUSG00000031072            2210010N10Rik,TAOS1,Oraov1
##                                                        REFSEQ
##                                                        <list>
## ENSMUSG00000035385                        NM_011333,NP_035463
## ENSMUSG00000039518 NM_001008424,NP_001008424,XM_006524543,...
## ENSMUSG00000036144                        NM_008584,NP_032610
## ENSMUSG00000027792       NM_009738,NP_033868,XM_011240000,...
## ENSMUSG00000022231       NM_009154,NP_033180,XM_006520043,...
## ENSMUSG00000031072       NM_028184,NP_082460,XM_006508649,...
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000035385 AAA37684,AAA37685,AAF15379,...
## ENSMUSG00000039518 AA562785,AAH55373,AK133029,...
## ENSMUSG00000036144 AAH02076,AAP32018,AK028352,...
## ENSMUSG00000027792 AAA37328,AAH99977,AK050337,...
## ENSMUSG00000022231 AAH65137,AK031231,AK033613,...
## ENSMUSG00000031072 AAH06906,AAH13564,AAO13812,...
DGE_analysis("Mouse d28_ctrlvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 12 rows and 5 columns
##                             treatment    donor     time replicate
##                              <factor> <factor> <factor>  <factor>
## BD330_Ctrl_D28mousegenes         mock   HU1019      d28          
## BD330_HBV_D28mousegenes           HBV   HU1019      d28          
## BD405A_Ctrl_D28mousegenes        mock   HU1020      d28          
## BD405A_HBV_D28mousegenes          HBV   HU1020      d28          
## Ctrl_D28_sample_1mousegenes      mock   HU1007      d28         a
## ...                               ...      ...      ...       ...
## HBV_D28_sample_1mousegenes        HBV   HU1007      d28         a
## HBV_D28_sample_2mousegenes        HBV   HU1007      d28         b
## HBV_D28_sample_3mousegenes        HBV   HU1007      d28          
## HU1016 Ctrl D28mousegenes        mock   HU1016      d28          
## HU1016_B_D28mousegenes            HBV   HU1016      d28          
##                             sizeFactor
##                              <numeric>
## BD330_Ctrl_D28mousegenes     1.3009710
## BD330_HBV_D28mousegenes      0.5694832
## BD405A_Ctrl_D28mousegenes    1.1260174
## BD405A_HBV_D28mousegenes     0.8927813
## Ctrl_D28_sample_1mousegenes  0.6416672
## ...                                ...
## HBV_D28_sample_1mousegenes   1.1035405
## HBV_D28_sample_2mousegenes   1.2618667
## HBV_D28_sample_3mousegenes   0.8042829
## HU1016 Ctrl D28mousegenes    1.7595897
## HU1016_B_D28mousegenes       1.1915768
## 
## [[2]]
## log2 fold change (MAP): treatment HBV vs mock 
## Wald test p-value: treatment HBV vs mock 
## DataFrame with 6 rows and 12 columns
##                       baseMean log2FoldChange     lfcSE      stat
##                      <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000029838  4846.94016      0.9185637 0.1641840  5.594720
## ENSMUSG00000074934   775.80079     -0.6098879 0.1236597 -4.931984
## ENSMUSG00000021596   103.32692     -0.8101245 0.1735435 -4.668136
## ENSMUSG00000024913  8130.06210      0.5824642 0.1353846  4.302293
## ENSMUSG00000064341 27893.63028      0.4607397 0.1107244  4.161138
## ENSMUSG00000028718    70.92816     -0.7083442 0.1799058 -3.937307
##                          pvalue         padj ENTREZID SYMBOL
##                       <numeric>    <numeric>   <list> <list>
## ENSMUSG00000029838 2.209784e-08 0.0004980411    19242    Ptn
## ENSMUSG00000074934 8.139841e-07 0.0091727868    23892  Grem1
## ENSMUSG00000021596 3.039451e-06 0.0228343796    78771  Mctp1
## ENSMUSG00000024913 1.690392e-05 0.0952451526    16973   Lrp5
## ENSMUSG00000064341 3.166653e-05 0.1427400355    17716    ND1
## ENSMUSG00000028718 8.240102e-05 0.2908543705    20460   Stil
##                                                              GENENAME
##                                                                <list>
## ENSMUSG00000029838                                       pleiotrophin
## ENSMUSG00000074934               gremlin 1, DAN family BMP antagonist
## ENSMUSG00000021596               multiple C2 domains, transmembrane 1
## ENSMUSG00000024913 low density lipoprotein receptor-related protein 5
## ENSMUSG00000064341                       NADH dehydrogenase subunit 1
## ENSMUSG00000028718                        Scl/Tal1 interrupting locus
##                                    ALIAS
##                                   <list>
## ENSMUSG00000029838  HARP,HB-GAM,HBBN,...
## ENSMUSG00000074934 Cktsf1b1,Drm,Grem,...
## ENSMUSG00000021596   2810465F10Rik,Mctp1
## ENSMUSG00000024913     BMND1,HBM,LR3,...
## ENSMUSG00000064341                   ND1
## ENSMUSG00000028718              Sil,Stil
##                                                        REFSEQ
##                                                        <list>
## ENSMUSG00000029838       NM_008973,NP_032999,XM_006505757,...
## ENSMUSG00000074934       NM_011824,NP_035954,XM_006499444,...
## ENSMUSG00000021596       NM_030174,NP_084450,XM_006517462,...
## ENSMUSG00000024913              NM_008513,NP_032539,XR_388250
## ENSMUSG00000064341                                  NP_904328
## ENSMUSG00000028718 NM_001304551,NM_001304553,NM_001304555,...
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000029838 AAB21834,AAH02064,AAH61695,...
## ENSMUSG00000074934 AAC40111,AAD54056,AAD54057,...
## ENSMUSG00000021596 AK013379,AK047562,AK054478,...
## ENSMUSG00000024913 AAC36468,AAC70183,AAH11374,...
## ENSMUSG00000064341 AAN85122,AAP89023,AAR21195,...
## ENSMUSG00000028718 AAC52386,AAH04585,AAH49865,...
##uninfected control cells versus those co-infected with HBV and HDV
DGE_analysis("Mouse d8_ctrlvcoinf")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                        treatment    donor     time
##                                         <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1mousegenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 2mousegenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 3mousegenes     coinf   HU1019       d8
## BD330_Ctrl_D8mousegenes                     mock   HU1019       d8
## BD330_HBV_HDV_D8_amousegenes               coinf   HU1019       d8
## ...                                          ...      ...      ...
## Ctrl_D8_sample_1mousegenes                  mock   HU1007       d8
## Ctrl_D8_sample_2mousegenes                  mock   HU1007       d8
## Ctrl_D8_sample_3mousegenes                  mock   HU1007       d8
## HU1016 Ctrl D8mousegenes                    mock   HU1016       d8
## HU1016_BD_co_D8mousegenes                  coinf   HU1016       d8
##                                        replicate sizeFactor
##                                         <factor>  <numeric>
## BD330 HBV_HDV Day 8 sample 1mousegenes         c  0.8269965
## BD330 HBV_HDV Day 8 sample 2mousegenes         d  0.8982170
## BD330 HBV_HDV Day 8 sample 3mousegenes         e  0.6922215
## BD330_Ctrl_D8mousegenes                           1.2863206
## BD330_HBV_HDV_D8_amousegenes                   a  0.7531468
## ...                                          ...        ...
## Ctrl_D8_sample_1mousegenes                     a   1.438224
## Ctrl_D8_sample_2mousegenes                     b   1.621194
## Ctrl_D8_sample_3mousegenes                         1.387785
## HU1016 Ctrl D8mousegenes                           1.116317
## HU1016_BD_co_D8mousegenes                          1.061993
## 
## [[2]]
## log2 fold change (MAP): treatment coinf vs mock 
## Wald test p-value: treatment coinf vs mock 
## DataFrame with 6 rows and 12 columns
##                      baseMean log2FoldChange     lfcSE      stat
##                     <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000036158  219.08223      1.1711543 0.1847361  6.339606
## ENSMUSG00000038393 6158.30436     -0.8535824 0.1753516 -4.867833
## ENSMUSG00000050578  215.43878     -1.0891644 0.2352736 -4.629352
## ENSMUSG00000021750   73.55790      1.0797301 0.2336259  4.621620
## ENSMUSG00000026475   62.05723     -1.0034907 0.2166718 -4.631385
## ENSMUSG00000000392    5.78075     -0.8571356 0.1836560 -4.667070
##                          pvalue         padj ENTREZID   SYMBOL
##                       <numeric>    <numeric>   <list>   <list>
## ENSMUSG00000036158 2.303542e-10 3.989044e-06   106042 Prickle1
## ENSMUSG00000038393 1.128288e-06 9.769278e-03    56338    Txnip
## ENSMUSG00000050578 3.668122e-06 1.098925e-02    17386    Mmp13
## ENSMUSG00000021750 3.807559e-06 1.098925e-02   268709  Fam107a
## ENSMUSG00000026475 3.632279e-06 1.098925e-02    19734    Rgs16
## ENSMUSG00000000392 3.055248e-06 1.098925e-02    14089      Fap
##                                                         GENENAME
##                                                           <list>
## ENSMUSG00000036158        prickle planar cell polarity protein 1
## ENSMUSG00000038393               thioredoxin interacting protein
## ENSMUSG00000050578                    matrix metallopeptidase 13
## ENSMUSG00000021750 family with sequence similarity 107, member A
## ENSMUSG00000026475           regulator of G-protein signaling 16
## ENSMUSG00000000392                 fibroblast activation protein
##                                                 ALIAS
##                                                <list>
## ENSMUSG00000036158 1110058P22Rik,AW215793,Prickle,...
## ENSMUSG00000038393 1200008J08Rik,AA682105,Hyplip1,...
## ENSMUSG00000050578                Clg,MMP-13,Mmp1,...
## ENSMUSG00000021750                       DRR1,Fam107a
## ENSMUSG00000026475                   Rgs14,Rgsr,Rgs16
## ENSMUSG00000000392                           SIMP,Fap
##                                                        REFSEQ
##                                                        <list>
## ENSMUSG00000036158 NM_001033217,NP_001028389,XM_006520264,...
## ENSMUSG00000038393    NM_001009935,NM_023719,NP_001009935,...
## ENSMUSG00000050578                        NM_008607,NP_032633
## ENSMUSG00000021750       NM_183187,NP_899010,XM_006518019,...
## ENSMUSG00000026475                        NM_011267,NP_035397
## ENSMUSG00000000392       NM_007986,NP_032012,XM_006498746,...
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000036158 AAH23970,AAI17893,AAI17894,...
## ENSMUSG00000038393 AAD48499,AAG32665,AAG32666,...
## ENSMUSG00000050578 AAI25321,AAI25323,AAT46404,...
## ENSMUSG00000021750 AAH55107,AK044219,AK083253,...
## ENSMUSG00000026475 AAB50619,AAC16913,AAC52927,...
## ENSMUSG00000000392 AAH19190,AK051959,AK136578,...
DGE_analysis("Mouse d28_ctrlvcoinf")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                         treatment    donor     time
##                                          <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1mousegenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 2mousegenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 3mousegenes     coinf   HU1019      d28
## BD330_Ctrl_D28mousegenes                     mock   HU1019      d28
## BD330_HBV_HDV_D28_bmousegenes               coinf   HU1019      d28
## ...                                           ...      ...      ...
## Ctrl_D28_sample_1mousegenes                  mock   HU1007      d28
## Ctrl_D28_sample_2mousegenes                  mock   HU1007      d28
## Ctrl_D28_sample_3mousegenes                  mock   HU1007      d28
## HU1016 Ctrl D28mousegenes                    mock   HU1016      d28
## HU1016_BD_co_D28mousegenes                  coinf   HU1016      d28
##                                         replicate sizeFactor
##                                          <factor>  <numeric>
## BD330 HBV_HDV Day 28 sample 1mousegenes         c  0.8988611
## BD330 HBV_HDV Day 28 sample 2mousegenes         d  1.0578876
## BD330 HBV_HDV Day 28 sample 3mousegenes         e  1.1254465
## BD330_Ctrl_D28mousegenes                           1.2183718
## BD330_HBV_HDV_D28_bmousegenes                   b  1.1926363
## ...                                           ...        ...
## Ctrl_D28_sample_1mousegenes                     a  0.5782738
## Ctrl_D28_sample_2mousegenes                     b  0.9196221
## Ctrl_D28_sample_3mousegenes                        0.9683076
## HU1016 Ctrl D28mousegenes                          1.6579823
## HU1016_BD_co_D28mousegenes                         0.9963621
## 
## [[2]]
## log2 fold change (MAP): treatment coinf vs mock 
## Wald test p-value: treatment coinf vs mock 
## DataFrame with 6 rows and 12 columns
##                      baseMean log2FoldChange     lfcSE      stat
##                     <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000033491  147.01899      0.9227285 0.1992539  4.630919
## ENSMUSG00000026399  128.08315      0.9116428 0.2194460  4.154293
## ENSMUSG00000017493 1706.66225     -0.8752717 0.2075056 -4.218063
## ENSMUSG00000037820  126.63093     -0.8425417 0.2011891 -4.187810
## ENSMUSG00000106944   19.85382      0.7458254 0.1785755  4.176527
## ENSMUSG00000038963   83.01172      0.7544383 0.1889308  3.993200
##                          pvalue       padj ENTREZID  SYMBOL
##                       <numeric>  <numeric>   <list>  <list>
## ENSMUSG00000033491 3.640456e-06 0.08107295   244954  Prss35
## ENSMUSG00000026399 3.262953e-05 0.14533192    13136    Cd55
## ENSMUSG00000017493 2.464101e-05 0.14533192    16010  Igfbp4
## ENSMUSG00000037820 2.816595e-05 0.14533192    21817    Tgm2
## ENSMUSG00000106944 2.959930e-05 0.14533192       NA      NA
## ENSMUSG00000038963 6.518753e-05 0.24195438   108115 Slco4a1
##                                                                       GENENAME
##                                                                         <list>
## ENSMUSG00000033491                                         protease, serine 35
## ENSMUSG00000026399     CD55 molecule, decay accelerating factor for complement
## ENSMUSG00000017493                insulin-like growth factor binding protein 4
## ENSMUSG00000037820                           transglutaminase 2, C polypeptide
## ENSMUSG00000106944                                                          NA
## ENSMUSG00000038963 solute carrier organic anion transporter family, member 4a1
##                                        ALIAS
##                                       <list>
## ENSMUSG00000033491 6030424L22Rik,P3D9,Prss35
## ENSMUSG00000026399      Daf,Daf-GPI,Daf1,...
## ENSMUSG00000017493 AI875747,Deb2,IGFBP-4,...
## ENSMUSG00000037820      G[a]h,TG2,TGase2,...
## ENSMUSG00000106944                        NA
## ENSMUSG00000038963   OATP-E,Slc21a12,Slco4a1
##                                                  REFSEQ
##                                                  <list>
## ENSMUSG00000033491 NM_178738,NP_848853,XM_006511170,...
## ENSMUSG00000026399 NM_010016,NP_034146,XM_006529115,...
## ENSMUSG00000017493                  NM_010517,NP_034647
## ENSMUSG00000037820                  NM_009373,NP_033399
## ENSMUSG00000106944                                   NA
## ENSMUSG00000038963 NM_148933,NP_683735,XM_006500547,...
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000033491 AAH75675,ABB46197,AK030671,...
## ENSMUSG00000026399 AAB00091,AAD51447,AAD51449,...
## ENSMUSG00000017493 AAH19836,AK003243,AK031212,...
## ENSMUSG00000037820 AAA40420,AAC62014,AAD37501,...
## ENSMUSG00000106944                             NA
## ENSMUSG00000038963 AAH30719,AAH30720,AAH33602,...
##monoinfected cells (HBV only) versus those co-infected with HBV and HDV
DGE_analysis("Mouse d8_coinfvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                        treatment    donor     time
##                                         <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1mousegenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 2mousegenes     coinf   HU1019       d8
## BD330 HBV_HDV Day 8 sample 3mousegenes     coinf   HU1019       d8
## BD330_HBV_D8mousegenes                       HBV   HU1019       d8
## BD330_HBV_HDV_D8_amousegenes               coinf   HU1019       d8
## ...                                          ...      ...      ...
## HBV_D8_sample_1mousegenes                    HBV   HU1007       d8
## HBV_D8_sample_2mousegenes                    HBV   HU1007       d8
## HBV_D8_sample_3mousegenes                    HBV   HU1007       d8
## HU1016_BD_co_D8mousegenes                  coinf   HU1016       d8
## HU1016_B_D8mousegenes                        HBV   HU1016       d8
##                                        replicate sizeFactor
##                                         <factor>  <numeric>
## BD330 HBV_HDV Day 8 sample 1mousegenes         c  0.8517347
## BD330 HBV_HDV Day 8 sample 2mousegenes         d  0.9272059
## BD330 HBV_HDV Day 8 sample 3mousegenes         e  0.7144467
## BD330_HBV_D8mousegenes                            0.9254134
## BD330_HBV_HDV_D8_amousegenes                   a  0.7785908
## ...                                          ...        ...
## HBV_D8_sample_1mousegenes                      a   1.795777
## HBV_D8_sample_2mousegenes                      b   1.226536
## HBV_D8_sample_3mousegenes                          1.762998
## HU1016_BD_co_D8mousegenes                          1.100822
## HU1016_B_D8mousegenes                              1.024806
## 
## [[2]]
## log2 fold change (MAP): treatment coinf vs HBV 
## Wald test p-value: treatment coinf vs HBV 
## DataFrame with 6 rows and 12 columns
##                      baseMean log2FoldChange     lfcSE      stat
##                     <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000034115   52.84019      2.3885023 0.3142402  7.600880
## ENSMUSG00000036144  401.07299      2.0072207 0.2903875  6.912214
## ENSMUSG00000028760  201.71111     -1.1454251 0.1958018 -5.849922
## ENSMUSG00000038393 5942.75005     -0.8608777 0.1535069 -5.608073
## ENSMUSG00000027875   88.99761     -1.6093765 0.2939548 -5.474912
## ENSMUSG00000048489   94.70841     -1.5419523 0.2955123 -5.217896
##                          pvalue         padj ENTREZID        SYMBOL
##                       <numeric>    <numeric>   <list>        <list>
## ENSMUSG00000034115 2.941230e-14 4.367727e-10    24046        Scn11a
## ENSMUSG00000036144 4.771466e-12 3.542813e-08    17286         Meox2
## ENSMUSG00000028760 4.918026e-09 2.434423e-05   230861        Eif4g3
## ENSMUSG00000038393 2.045918e-08 7.595471e-05    56338         Txnip
## ENSMUSG00000027875 4.377286e-08 1.300054e-04    15360        Hmgcs2
## ENSMUSG00000048489 1.809667e-07 4.478925e-04   213393 8430408G22Rik
##                                                               GENENAME
##                                                                 <list>
## ENSMUSG00000034115       sodium channel, voltage-gated, type XI, alpha
## ENSMUSG00000036144                               mesenchyme homeobox 2
## ENSMUSG00000028760 eukaryotic translation initiation factor 4 gamma, 3
## ENSMUSG00000038393                     thioredoxin interacting protein
## ENSMUSG00000027875    3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2
## ENSMUSG00000048489                          RIKEN cDNA 8430408G22 gene
##                                                         ALIAS
##                                                        <list>
## ENSMUSG00000034115                           NSS2,NaN,NaT,...
## ENSMUSG00000036144                     AI528662,Gax,Mox-2,...
## ENSMUSG00000028760 1500002J22Rik,4833436O05,4930523M17Rik,...
## ENSMUSG00000038393         1200008J08Rik,AA682105,Hyplip1,...
## ENSMUSG00000027875                      1300002P16,mHS,Hmgcs2
## ENSMUSG00000048489                    Depp,Fseg,8430408G22Rik
##                                                     REFSEQ
##                                                     <list>
## ENSMUSG00000034115    NM_011887,NP_036017,XM_017313362,...
## ENSMUSG00000036144                     NM_008584,NP_032610
## ENSMUSG00000028760 NM_001256195,NM_001256198,NM_172703,...
## ENSMUSG00000038393 NM_001009935,NM_023719,NP_001009935,...
## ENSMUSG00000027875                     NM_008256,NP_032282
## ENSMUSG00000048489 NM_001166580,NM_145980,NP_001160052,...
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000034115 AAD53403,AAO85711,AB031389,...
## ENSMUSG00000036144 AAH02076,AAP32018,AK028352,...
## ENSMUSG00000028760 AAH23898,AAH47531,AAH48848,...
## ENSMUSG00000038393 AAD48499,AAG32665,AAG32666,...
## ENSMUSG00000027875 AAA92675,AAA92676,AAH14714,...
## ENSMUSG00000048489 AAH31533,AAH58515,AB024924,...
DGE_analysis("Mouse d28_coinfvHBV")
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates

## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns

## [[1]]
## DataFrame with 16 rows and 5 columns
##                                         treatment    donor     time
##                                          <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1mousegenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 2mousegenes     coinf   HU1019      d28
## BD330 HBV_HDV Day 28 sample 3mousegenes     coinf   HU1019      d28
## BD330_HBV_D28mousegenes                       HBV   HU1019      d28
## BD330_HBV_HDV_D28_bmousegenes               coinf   HU1019      d28
## ...                                           ...      ...      ...
## HBV_D28_sample_1mousegenes                    HBV   HU1007      d28
## HBV_D28_sample_2mousegenes                    HBV   HU1007      d28
## HBV_D28_sample_3mousegenes                    HBV   HU1007      d28
## HU1016_BD_co_D28mousegenes                  coinf   HU1016      d28
## HU1016_B_D28mousegenes                        HBV   HU1016      d28
##                                         replicate sizeFactor
##                                          <factor>  <numeric>
## BD330 HBV_HDV Day 28 sample 1mousegenes         c  0.9545548
## BD330 HBV_HDV Day 28 sample 2mousegenes         d  1.1207982
## BD330 HBV_HDV Day 28 sample 3mousegenes         e  1.1965253
## BD330_HBV_D28mousegenes                            0.5608572
## BD330_HBV_HDV_D28_bmousegenes                   b  1.2679145
## ...                                           ...        ...
## HBV_D28_sample_1mousegenes                      a  1.0801663
## HBV_D28_sample_2mousegenes                      b  1.2219894
## HBV_D28_sample_3mousegenes                         0.7671387
## HU1016_BD_co_D28mousegenes                         1.0579929
## HU1016_B_D28mousegenes                             1.1896661
## 
## [[2]]
## log2 fold change (MAP): treatment coinf vs HBV 
## Wald test p-value: treatment coinf vs HBV 
## DataFrame with 6 rows and 12 columns
##                      baseMean log2FoldChange     lfcSE      stat
##                     <numeric>      <numeric> <numeric> <numeric>
## ENSMUSG00000049093   36.18814       2.326889 0.3518473  6.613351
## ENSMUSG00000027656  485.45875      -2.049403 0.3242750 -6.319953
## ENSMUSG00000037370  128.75418       1.842799 0.3010990  6.120242
## ENSMUSG00000018830   86.33487      -1.803739 0.3054746 -5.904709
## ENSMUSG00000006014   55.49869      -1.990055 0.3455553 -5.759006
## ENSMUSG00000026822 1405.67824      -1.841151 0.3274374 -5.622911
##                          pvalue         padj ENTREZID SYMBOL
##                       <numeric>    <numeric>   <list> <list>
## ENSMUSG00000049093 3.757163e-11 5.184133e-07   209590  Il23r
## ENSMUSG00000027656 2.616426e-10 1.805072e-06    22403  Wisp2
## ENSMUSG00000037370 9.343331e-10 4.297309e-06    18605  Enpp1
## ENSMUSG00000018830 3.532690e-09 1.218601e-05    17880  Myh11
## ENSMUSG00000006014 8.461072e-09 2.334917e-05    96875   Prg4
## ENSMUSG00000026822 1.877663e-08 4.317999e-05    16819   Lcn2
##                                                                                                 GENENAME
##                                                                                                   <list>
## ENSMUSG00000049093                                                               interleukin 23 receptor
## ENSMUSG00000027656                                            WNT1 inducible signaling pathway protein 2
## ENSMUSG00000037370                                    ectonucleotide pyrophosphatase/phosphodiesterase 1
## ENSMUSG00000018830                                           myosin, heavy polypeptide 11, smooth muscle
## ENSMUSG00000006014 proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)
## ENSMUSG00000026822                                                                           lipocalin 2
##                                                ALIAS
##                                               <list>
## ENSMUSG00000049093                      IL-23R,Il23r
## ENSMUSG00000027656              Ccn5,Crgr4,Ctgfl,...
## ENSMUSG00000037370 4833416E15Rik,AI428932,C76301,...
## ENSMUSG00000018830              AV071570,SM1,SM2,...
## ENSMUSG00000006014               CACP,DOL54,JCAP,...
## ENSMUSG00000026822             24p3,AW212229,NRL,...
##                                                     REFSEQ
##                                                     <list>
## ENSMUSG00000049093                     NM_144548,NP_653131
## ENSMUSG00000027656    NM_016873,NP_058569,XM_006499169,...
## ENSMUSG00000037370 NM_001308327,NM_001308329,NM_008813,...
## ENSMUSG00000018830 NM_001161775,NM_013607,NP_001155247,...
## ENSMUSG00000006014 NM_001110146,NM_021400,NP_001103616,...
## ENSMUSG00000026822                     NM_008491,NP_032517
##                                            ACCNUM
##                                            <list>
## ENSMUSG00000049093 AAI12426,AAM44230,AF461423,...
## ENSMUSG00000027656 AAC96320,AAD18058,AAH32877,...
## ENSMUSG00000037370 AAA39892,AAA39893,AAI60371,...
## ENSMUSG00000018830 AAA67552,AAB36168,AAH26142,...
## ENSMUSG00000006014 AAI30022,AB034730,AK132597,...
## ENSMUSG00000026822 AAA79309,AAI32070,AAI32072,...

Session Info

sessionInfo()
## R version 3.3.3 (2017-03-06)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Sierra 10.12.6
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] org.Mm.eg.db_3.4.0         AnnotationDbi_1.36.2      
##  [3] BiocInstaller_1.24.0       viridis_0.5.1             
##  [5] viridisLite_0.3.0          ggrepel_0.8.0             
##  [7] data.table_1.11.4          genefilter_1.56.0         
##  [9] RColorBrewer_1.1-2         gplots_3.0.1              
## [11] DESeq2_1.14.1              SummarizedExperiment_1.4.0
## [13] Biobase_2.34.0             GenomicRanges_1.26.4      
## [15] GenomeInfoDb_1.10.3        IRanges_2.8.2             
## [17] S4Vectors_0.12.2           BiocGenerics_0.20.0       
## [19] openxlsx_4.1.0             reshape2_1.4.3            
## [21] ggplot2_3.0.0              stringr_1.3.1             
## [23] dplyr_0.7.6               
## 
## loaded via a namespace (and not attached):
##  [1] bit64_0.9-7         splines_3.3.3       gtools_3.8.1       
##  [4] Formula_1.2-3       assertthat_0.2.0    latticeExtra_0.6-28
##  [7] blob_1.1.1          yaml_2.2.0          pillar_1.3.0       
## [10] RSQLite_2.1.1       backports_1.1.2     lattice_0.20-35    
## [13] glue_1.3.0          digest_0.6.15       XVector_0.14.1     
## [16] checkmate_1.8.5     colorspace_1.3-2    htmltools_0.3.6    
## [19] Matrix_1.2-8        plyr_1.8.4          XML_3.98-1.12      
## [22] pkgconfig_2.0.1     zlibbioc_1.20.0     purrr_0.2.5        
## [25] xtable_1.8-2        scales_0.5.0        gdata_2.18.0       
## [28] BiocParallel_1.8.2  tibble_1.4.2        htmlTable_1.12     
## [31] annotate_1.52.1     withr_2.1.2         nnet_7.3-12        
## [34] lazyeval_0.2.1      survival_2.42-6     magrittr_1.5       
## [37] crayon_1.3.4        memoise_1.1.0       evaluate_0.11      
## [40] foreign_0.8-71      tools_3.3.3         locfit_1.5-9.1     
## [43] munsell_0.5.0       cluster_2.0.5       zip_1.0.0          
## [46] bindrcpp_0.2.2      caTools_1.17.1.1    rlang_0.2.1        
## [49] grid_3.3.3          RCurl_1.95-4.11     rstudioapi_0.7     
## [52] htmlwidgets_1.2     bitops_1.0-6        base64enc_0.1-3    
## [55] rmarkdown_1.10      gtable_0.2.0        DBI_1.0.0          
## [58] R6_2.2.2            gridExtra_2.3       knitr_1.20         
## [61] bit_1.1-14          bindr_0.1.1         Hmisc_4.1-1        
## [64] rprojroot_1.3-2     KernSmooth_2.23-15  stringi_1.2.4      
## [67] Rcpp_0.12.18        geneplotter_1.52.0  rpart_4.1-13       
## [70] acepack_1.4.1       tidyselect_0.2.4